2. cochemical restrictions. Correspondingly, we present below
a description of the evolution of precursor sets that had been
initially designed with respect to specific medicinal chemistry
objectives and that have subsequently been modified to
accommodate the reactivity and physicochemical require-
ments of a specific, automated chemical transformation,
namely, the Mitsunobu reaction.
Precursor Set Design
The compound inventory discussed above consists of sets
of compounds grouped primarily by reactive functionality.
We will comment in future publications on the overall design
of this inventory but limit ourselves here to a discussion of
the characteristics of two precursor collections: a set of
homologous aliphatic alcohols and a diverse set of phenols.
In the case of the former, we assembled a series of primary,
secondary, and tertiary aliphatic alcohols containing the
functionality typically employed to probe nonaromatic
hydrophobic interactions.11
Thus, the set consists of a
homologous series of linear, branched, cyclic, and fused-
cyclic analogues. In addition, a limited number of bioisosteric
replacements of methylenes and various degrees of unsat-
uration have been included to expand the property space
covered by the set. The collection is shown in Figure 1.
By contrast, we designed a set of structurally diverse
phenols (Figure 2) based on compounds listed in the
Available Chemicals Directory (ACD).12
In selecting precur-
sors, we decided to use a molecular weight cutoff of 210.
This was based on an average molecular weight of 290 for
compounds submitted to our group for derivatization and a
desire that the bulk of the products synthesized be consistent
with Lipinski’s rule of five.13
This reduced the ACD file of
available phenols from an initial set of 13 453 down to 2288
compounds. Additionally, all radiolabeled phenols were
removed, further reducing the set to 2125 compounds. This
collection was then used to perform a cluster analysis14
using
Figure 1. Original aliphatic alcohol collection.
Protocols and Precursor Sets Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 443
3. as a basis a set of 100 clusters. This number was used on
the basis of a subjective assessment of the homology between
compounds grouped within a given cluster. An alternative
analysis using smaller numbers of clusters resulted in
significantly distinct structures being grouped together. The
result of this 100-cluster-set analysis is shown in Figure 3,
which depicts the population numbers associated with each
cluster. This distribution was used as a reference with which
to compare subsequent selections of compounds.
To this set we applied the selection process outlined in
Table 1. We adopted a procedure that first involved removing
compounds that were inappropriate from a medicinal chem-
istry perspective, sequentially excluding all alkylating re-
agents, Michael acceptors, excessively halogenated precur-
sors, and phenols with long alkyl chain substituents. This,
together with the elimination of radiolabeled precursors,
resulted in the elimination of 312 compounds. We next
removed compounds that were anticipated to be problematic
under the conditions of the Mitsunobu reaction, from either
a chemo- or a regioselectivity perspective. This resulted in
the elimination of sets of acids, aldehydes, o-aminophenols,
Figure 2. Diversity phenol collection.
Figure 3. Commercially available phenols. MW < 210.
444 Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 Gentles et al.
4. sulfonamides, polyhydroxylated phenols, hydroxamic acids,
and a number of salts. This filter removed a further 746
compounds from the file and reduced the number of usable
phenols to 1311. Table 1 lists the number of compounds
excluded by each of the above-mentioned criteria.
An examination of the consequences of the removal of
the above compounds was assessed by examining which
clusters from the original distribution shown in Figure 3 were
no longer represented in the residual selection. The distribu-
tions of the phenols left after removal of compounds with
biological and chemical liabilities are shown in Figures 4
and 5, respectively. It is apparent that the biological compat-
ibility filter excluded only two clusters, 21 and 64, corre-
sponding respectively to sets of vinylnitro and substituted
acrylonitrile compounds. The chemistry compatibility filter
that had excluded a much larger number of compounds
surprisingly also resulted in the loss of only two clusters,
52 and 66, corresponding to sets of 1,2-aliphatic hydroxy-
aminophenols and a class of triazole substituted phenols.
However, a further restriction on our precursor set was the
decision to limit compound selection based on multigram
availability from major chemical vendors. This filter resulted
in the elimination of 33 of the original 100 clusters, the
distribution profile of the residual 64 clusters being shown
as the taller columns at the rear of the plot in Figure 6. It is
apparent that this restriction is the single most significant
factor that impacts the range of diversity that can be accessed
using the strategy outlined here, much more so than the
elimination of compounds for reasons of biological or
chemical compliance. However, given that ultimately we
have to select only 48 compounds (i.e., the number that can
be run on our automation platform), we planned to use
reaction yield as a final filtering criterion. Therefore, we
selected one member from each of the residual 64 clusters
for the chemical optimization process outlined below.
Ultimately, we would select 48 precursors based on the 48
highest yielding reactions. This would ensure that each
compound selected originated from a different cluster of the
original set of 100 clusters and should provide a set of
reagents with a good overall reactivity profile.
With sets of focused aliphatic alcohols and diversity
phenols identified, we proceeded to implement an automated
chemistry protocol.
Results and Discussion
The Mitsunobu reaction has found extensive application
in combinatorial chemistry,16
providing a method for the
generation of molecular diversity through the use of alcohols
in combination with phenols and other acidic precursors.17
While many articles have been published on the methodology
of this reaction, we chose to follow a recently reported
procedure that exploits resin-supported triphenylphosphine
Table 1. Selection Criteria for Phenols
biological incompatibility filter eliminated chemical incompatibility filter eliminated
alkyl halides 11 acids 337
deuterated phenols 65 aldehydes 121
tritiated phenols 24 o-aminophenols 70
13C-labeled phenols 50 aliphatic alcohols 112
14C-labeled phenols 54 sulfonamides 4
Si-containing phenols 1 thiols 18
sulfonic acids and esters 13 incompatible salts 26
polynitrophenols 19 poly-OH-phenols 47
polyhalogentated (>4) phenols 13 hydroxamic acids 7
Michael acceptors + long-chain alkyls 62 imides 4
totals 312 746
Figure 4. Biologically compliant phenols.
Figure 5. Commercially compliant phenols.
Figure 6. Commercial phenols and selected precursors.
Protocols and Precursor Sets Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 445
5. (PS-PPh3) and di-tert-butylazodicarboxylate (DBAD) as the
redox partners.18
It had been demonstrated that this combina-
tion has distinct advantages in terms of ease of isolation of
the products and seemed to be the most easily adaptable for
implementation on our automation platform.
Consequently, a series of experiments was performed using
the phenol I and the alcohols A1, A14, A37, and A46 as
shown in Scheme 1. Compound I was chosen because it is
moderately deactivated, both electronically and sterically, and
was therefore thought to be a suitably demanding chemical
probe. The alcohols were chosen to be representative of the
chemical reactivity and physicochemical properties displayed
by the precursors shown in Figure 1. The purpose of these
experiments was to identify optimal bench conditions prior
to developing an automated procedure. This order of events
gave us a performance target in subsequently developing the
chemistry on the synthesizer, a strategy that allowed us to
distinguish between the limitations of the chemistry and those
of the automation platform.
Three key chemistry issues became apparent during this
development phase. The first related to the quality of the
triphenylphosphine resin used. It was found that resin from
different suppliers had different ratios of supported phosphine
to phosphine oxide, sufficient to require modifications to the
stoichiometries employed in the reaction. Importantly, it was
determined that the oxide impurity arose from aerial oxida-
tion19
and that resins supplied by different companies
demonstrated different degrees of oxygen sensitivity.20
For
the purposes of this work, we fixed on one supplier that
provided resin with consistent high loading of phosphine with
little or no related oxide, as determined by elemental analysis
and 31
P NMR.21
It was also helpful to open bottles of this
reagent just prior to the synthesis setup. Consistent with these
observations was the need to carefully exclude oxygen from
the reaction in order to optimize yields.
Other key development issues related to the observation
that secondary alcohols were, not unsurprisingly, consistently
less reactive than primary alcohols. However, it was found
that performing a double addition of DBAD and the
secondary alcohol precursor in the presence of a 2-fold excess
of the supported phosphine reagent compensated for the
reduced reactivity and resulted in significantly improved
reaction performance.18
Also, during this phase of the
protocol development, we explored the use of both DCM
and THF as reaction solvent and noted only minor differences
in the yields of products obtained. Interestingly, we also
determined that the introduction of up to 40% DMA as a
cosolvent did not significantly impact the efficiency of the
reaction. This was important because it greatly increased the
range of compounds that could be solubilized for derivati-
zation by this process. The optimized conditions identified
from these studies are described in Scheme 1.
Subsequently, these conditions were employed on our
automation platform using the same reaction partners shown
above. After significant optimization of the various pipetting
and transfer processes involved in the automated synthesis,
a high degree of correlation between the bench and auto-
mated processes was achieved, as shown by the data in Table
2. The newly developed automated protocol was then adapted
to run 48 reactions using the phenol I in combination with
the set of the precursors listed in Figure 1.
As was commented above, this set of alcohols was chosen
to investigate hydrophobic interactions in lead optimization
exercises and was not designed specifically for the Mitsunobu
protocol. Not unsurprisingly therefore, several failed to react.
Scheme 1
Table 2. Comparison of Manual and Automation Runs for
Aliphatic Monomers
446 Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 Gentles et al.
6. Most obvious were precursors A8, A13, and A38, all of
which contained a 3° alcohol functionality.17
Similarly,
compounds A42, A45, and A47 contain constrained 2°
alcohol groups, which would not be expected to invert readily
under the normal SN2 conditions of the Mitsunobu reaction.
In addition, precursors A29, A30, and A31 could be
anticipated to be prone to a competing β-elimination reaction
involving the activated oxyphosphonium intermediate,22
while the acidic alcohols A19 and A20 could be expected
to be inductively deactivated and therefore unreactive under
the conditions explored. It was also supposed that the
neopentyl system A15 would be prone to rearrangement,23
while the adamantyl alcohol precursor A48 was determined
to be too hindered to react under the conditions investigated.
These unreactive precursors where then replaced with
others more compatible with the conditions of the Mitsunobu
reaction. The substitutions were designed to retain as much
of the character of the original set as possible. This involved
replacement of terminal acetylenes with internal variants,
tertiary alcohols were replaced with sterically less hindered
but highly R-branched secondary analogues, and compounds
susceptible to β-elimination were replaced with others
containing substituents in positions not prone to such
reactions.
In addition to making replacements, it was helpful to
change the physical order of the precursors within the set
such that the less reactive 2° alcohols were grouped together.
This greatly facilitated the execution of the double addition
of reagents by the synthesizer, allowing the single addition
of DBAD and less reactive precursor first and allowing them
to react while the synthesizer was setting up the remaining
30 reactions using primary alcohols. On completion of the
initial pipetting operations, a suitable time delay had ensued
prior to the second addition of reagents to the subset of 2°
alcohols. Figure 9 shows the final order and content of the
optimized set of precursors, and the yields observed using
this reagent set are reported in Figure 7.
With these modifications, we achieved a reaction success
rate of 100% and the reaction yields across the set were
relatively uniform (SD ) 15%) and averaged 68%. It was
estimated that this represents a near-quantitative chemical
conversion, since we typically see peak-to-peak transforma-
tion of starting material to product by LC-MS, and in
independent experiments we have determined that we can
loose up to 25% of the product masses during the postsyn-
thesis sample manipulations required for analysis and
purification.
An exercise essentially identical to that outlined above was
then repeated using alcohol II shown in Scheme 2, in
combination with four phenolic probes representative of the
range of chemical reactivity of the set under investigation.
These reagents are shown in Table 3, with the optimal
reaction conditions being depicted at the bottom of Scheme
2. Attempts to vary the order of addition of reagents where-
by the phenolic reagents were introduced last resulted in
the formation of significant amounts of alkylated hydra-
zine derivatives.24 Thus, for both protocols, an identical order
of addition of reagents was observed. The optimized pro-
tocol was then transferred to our automation platform and
used to run reactions employing the previously selected set
of 64 phenols. The results for the highest yielding 48
reactions are shown in Figure 8, with the specific phenols
associated with these reactions shown in Figure 2. Their
position within the set and their original cluster assignment
are indicated by the letters P and C, respectively, and the
distribution of this set within the clusters of the original ACD
phenols is shown graphically as the smaller columns in
Figure 6.
In comparison with the aliphatic alcohol run, the average
yield was lower (60%) and the individual yields were slightly
more variable (SD ) 19%), as might be expected with a
diversity-based experiment covering a wider range of
reactants. However, these differences are less than might have
been expected, and the overall reaction performance is
obvious and gives an excellent indication of the generality
of the procedure.
Concluding Remarks
Given these results, it is apparent that the use of optimized
precursor sets significantly improves the performance of
automated chemical procedures, in terms of both the reaction
success rates and the overall yields of the syntheses. This
enhanced efficiency is significant in that it greatly increases
the applicability of this methodology to lead optimization
where larger sets of compounds can now be reliably prepared
from relatively small amounts of valuable starting materials.
We have also established that the co-optimization of precur-
sor sets in terms of experimental design and chemical
compliance is a realistic goal that does not require undue
Figure 7. Aliphatic alcohol precursors yields: average ) 71%;
SD ) 17%.
Figure 8. Phenolic precursor yields: average ) 60%; SD ) 19%.
Protocols and Precursor Sets Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 447
7. compromises to be made to the fundamental medicinal chem-
istry objectives. As regards the generality of the chemical
protocols, it should be noted that the phenols used in the
above experiments cover a wide range of structural classes
and related reactivities and therefore give a good indication
of the scope of this procedure. It is also apparent that such
optimized precursor sets have widespread application in a
number of problems in lead optimization, and in our
laboratories, they are the preferred method for performing
initial analogue exercises, particularly in the absence of
compelling structural information or extensive SAR data. We
will shortly report on the application of this strategy to other
reactions and alternative experimental designs.
Experimental Section
General. Starting materials, reagents, and solvents were
purchased from Aldrich Chemical Co., Milwaukee, WI,
unless otherwise stated and were used as supplied without
further purification. DBAD was purchased from Lancaster
Synthesis Inc., Windham, NH. In the case of PS-PPh3, only
newly opened bottles were used for all of the reactions
Figure 9. Optimized set of aliphatic alcohols for the Mitsunobu reaction.
Scheme 2
448 Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 Gentles et al.
8. described below. All 1
H NMR spectra were recorded on a
Varian Unity 500 plus NMR spectrometer, and chemical
shifts (δ) are reported in ppm relative to TMS as internal
standard. All samples were dissolved in CDCl3 unless
otherwise specified. Multiplicities are indicated as the
following: s, singlet; d, doublet; t, triplet; m, multiplet; dd,
doublet of doublets; ddd, doublet of doublet of doublets; br,
broad. Coupling constants (J values) where noted are quoted
in hertz. Low-resolution mass spectra were recorded using
a Finnigan DCI/MS SSQ7000 single-quadruple mass spec-
trometer. LC-MS analyses were performed using a Hewlett-
Packard HP1100 instrument fitted with photodiode array and
ELSD (SEDEX 55) detectors and employing the following
methods: solvent A of 0.1% TFA; solvent B of acetonitrile
(ACN); 4 min gradient of 10-95% B; column, YMC ODS-
AQ 2.0 mm × 50 mm cartridge; APCI positive ionization
to identify the mass ion. All parallel syntheses were
performed using a PE Biosystems (Applied Biosystems)
Solaris 530 organic synthesizer configured as supplied by
the manufacturer with the exception of precursor racks, which
were customized to accommodate a 6 × 4 array of 4 mL
precursor vials configured in a 96-well footprint format. All
precursors used in the automated synthesis were supplied as
either oils or solids in capped 4 mL Kimble vials (Kimble
60881A-1545, convenience pack) with each vial containing
0.6 mmol of material supplied directly from Aldrich Chemi-
cal Co. The synthesis scripts used to execute the automated
protocol are provided in the Supporting Information and are
annotated to facilitate an understanding of the logic of the
programming. All samples after synthesis were purified using
preparative reverse-phase HPLC employing a Waters Nova-
Pak HR C18 column (25 mm × 100 mm, 6 µm particle size)
using a gradient of 10-100% ACN, 0.1% aqueous TFA over
8 min (10 min run time) at a flow rate of 40 mL/min.
General Bench Protocol for the Synthesis of Aryl Alkyl
Ethers Using Aliphatic Alcohols as Precursors. PS-PPh3
resin (54 mg, 2.2 equiv for 1° alcohols; 108 mg, 4.4 equiv
for 2° alcohols) was added to a dried 20 mL scintillation
vial that was then capped and flushed with nitrogen. The
resin was suspended in 1 mL of anhydrous THF. After a
period of 2 min, the phenolic core I (15 mg, 0.073 mmol)
dissolved in 0.5 mL of anhydrous THF was added in a single
portion. The resultant suspension was mixed briefly, after
which a solution of DBAD (27 mg, 1.6 equiv) in 0.5 mL of
anhydrous THF was added in a single portion. This mixture
was then agitated on an orbital shaker for 3 min, after which
a solution of the alcohol precursor (1.25 equiv) in 1.0 mL
of anhydrous THF was added in a single portion. The
reaction mixture was then agitated for a period of 3 h. Then,
for 2° alcohols, additions of DBAD (27 mg in 0.5 mL of
anhydrous THF) and monomer (1.25 equiv in 0.5 mL of
anhydrous THF) were repeated. The stirring was maintained
for an additional 6 h. The resultant suspension was filtered,
and the resin was washed with THF (3 × 3 mL). The filtrate
and washings were combined and evaporated in vacuo, and
the weight of the crude reaction mixture was determined.
LC-MS analysis was performed on this mixture prior to
dissolving the residue in 1.5 mL of a 1:1 mixture of DMSO/
MeOH and to submitting to purification by preparative
reverse-phase HPLC. Homogeneous fractions were combined
and evaporated in vacuo, and the residue’s weight was
determined to calculate the yield of the reaction. Products
were typically obtained as amorphous solids or oils, and their
NMR and MS data were consistent with the desired
structures.
General Bench Protocol for the Synthesis of Aryl Alkyl
Ethers Using Phenols as Precursors. PS-PPh3 resin (60
mg, 2.2 equiv) was added to a dried 20 mL scintillation vial
that was then capped and flushed with nitrogen. The resin
was suspended in 1 mL of anhydrous THF. After a period
of 2 min, the phenolic precursor (1.5 equiv) dissolved in
0.5 mL of anhydrous THF was added in a single portion.
The resultant suspension was mixed briefly, after which a
solution of DBAD (30 mg, 1.6 equiv) in 0.5 mL of anhydrous
THF was added in a single portion. This mixture was then
agitated on an orbital shaker for 3 min, after which a solution
of the alcohol core II (15 mg, 0.081 mmol) in 1.0 mL of
anhydrous THF was added in a single portion. The reaction
mixture was then agitated for a period of 9 h. The resultant
suspension was filtered, and the resin was washed with THF
(3 × 3 mL). The filtrate and washings were combined and
evaporated in vacuo, and the weight of the crude reaction
mixture was determined. LC-MS analysis was performed
on this mixture prior to dissolving the residue in 1.5 mL of
a 1:1 mixture of DMSO/MeOH and to submitting to
purification by preparative reverse-phase HPLC. Homoge-
neous fractions were combined and evaporated in vacuo, and
the residue’s weight was determined to calculate the yield
of the reaction. Products were typically obtained as amor-
phous solids or oils, and their NMR and MS data were
consistent with the desired structures.
HCl Digest. The crude material obtained from evaporation
of solvents after the synthesis was treated with 4.0 mL of 4
M HCl in dioxane at room temperature for 4 h. The resulting
solution was evaporated in vacuo, and the workup was
continued as described above. The HCl digest was performed
to decompose the hydrazine byproduct formed from reduc-
tion of DBAD and was applied to crude materials from
automated runs employing the phenolic precursors P33-C39
and P39-C55, for which there was a possibility of a coelution
Table 3. Comparison of Manual and Automation Runs for
Phenolic Monomers
Protocols and Precursor Sets Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 449
9. of the byproduct and the resulting ether during HPLC
purification.
Automated Protocol for the Synthesis of Aryl Alkyl
Ethers Using the Aliphatic Alcohols as Precursors. For
2° Alcohols. A reaction vessel of the Solaris 530 synthesizer
was charged with PS-PPh3 resin (108 mg, 4.4 equiv) and
was purged by passing a stream of N2 for 45 s. A solution
of the phenolic core I (1.000 mL, 15 mg/mL) was added to
the vessel, and the resultant suspension was shaken for 15
min. A solution of DBAD (0.600 mL, 54 mg/mL) in
anhydrous THF was then added, the contents of the flask
were shaken for 10 min, and a solution of the alcohol
precursor (0.345 mL, 0.3 mM) was added. The resultant
suspension was shaken at room temperature for 3 h. The
addition of DBAD and monomer was then repeated, and the
agitation was maintained for an additional 6 h. The solution
was drained and transferred to a destination vial. The resin
was washed with 3.0, 3.5, and 3.5 mL of THF. The washes
were combined with the filtrate, and resultant solution was
processed as described before in the corresponding bench
protocol.
For 1° Alcohols. A reaction vessel of the Solaris 530
synthesizer was charged with PS-PPh3 resin (54 mg, 2.2
equiv) and was purged by passing a stream of N2 for 45 s.
A solution of the phenolic core I (1.000 mL, 15 mg/mL)
was added to the vessel, and the resultant suspension was
shaken for 15 min. A solution of DBAD (0.600 mL, 54 mg/
mL) in anhydrous THF was then added, and the contents of
the flask were shaken for 10 min prior to the addition of a
solution of the alcohol precursor (0.345 mL, 0.3 mM). The
resultant suspension was shaken at room temperature for 9
h. The solution was drained and transferred to a destination
vial. The resin was then washed with 2.5, 3.5, and 3.5 mL
of THF. The washes were combined with the filtrate, and
the resultant solution was processed as described before in
the corresponding bench protocol.
Automated Protocol for the Synthesis of Aryl Alkyl
Ethers Using the Phenols as Precursors. A reaction vessel
of the Solaris 530 synthesizer was charged with PS-PPh3
resin (60 mg, 2.2 equiv) and was purged by passing a stream
of N2 for 45 s. A solution of a phenolic precursor (0.410
mL, 0.3 mM solution) was added to the vessel, and the
resultant suspension was shaken for 15 min. A solution of
DBAD (0.600 mL, 60 mg/mL) in anhydrous THF was then
added, and the contents of the flask were shaken for 10 min
prior to the addition of a solution of the alcohol core II (1.000
mL, 15 mg/mL). The resultant suspension was shaken at
room temperature for 9 h. The solution was drained and
transferred to a destination vial. The resin was then washed
with 2.5, 3.5, and 3.5 mL of THF. The washes were
combined with the filtrate, and the resultant solution was
processed as described before in the corresponding bench
protocol.
For each synthesized compound, the following data are
provided: yield from the automated run, 1
H NMR data, MS
data, and retention time RT (min) for purified sample on the
analytical HPLC.
3-Chloro-4-isopropoxybiphenyl (derived from I and
AF1): 8.8 mg (51%); 1
H NMR (500 MHz, CDCl3) δ ppm
7.61 (d, J ) 2.2 Hz, 1H), 7.53 (m, 2H), 7.42 (m, 3H), 7.32
(m, 1H), 7.01 (d, J ) 8.4 Hz, 1H), 4.59 (m, 1H), 1.41 (d, J
) 5.9 Hz, 6H); MS (DCI/NH3) m/z 264 [M + NH4]+
; RT )
2.40.
3-Chloro-4-cyclobutyloxybiphenyl (derived from I and
AF2): 13.4 mg (74%); 1
H NMR (500 MHz, CDCl3) δ ppm
7.60 (d, J ) 2.2 Hz, 1H), 7.52 (m, 1H), 7.40 (m, 2H), 7.31
(m, 3H), 6.85 (m, 1H), 6.84 (d, J ) 8.7 Hz, 1H), 4.72 (m,
1H), 2.50 (m, 2H), 2.28 (m, 2H), 1.90 (m, 1H), 1.71 (m,
1H); MS (DCI/NH3) m/z 276 [M + NH4]+
; RT ) 2.48.
4-sec-Butoxy-3-chlorobiphenyl (derived from I and
AF3): 12.7 mg (70%); 1
H NMR (500 MHz, CDCl3) δ ppm
7.60 (d, J ) 2.2 Hz, 1H), 7.52 (m, 1H), 7.41 (m, 2H), 7.32
(m, 3H), 6.99 (d, J ) 8.4 Hz, 1H), 4.37 (m, 1H), 1.82 (m,
1H), 1.70 (m, 1H), 1.36 (d, J ) 5.9 Hz, 1H), 1.03 (t, J )
7.3 Hz, 1H); MS (DCI/NH3) m/z 278 [M + NH4]+
; RT )
2.53.
3-Chloro-4-cyclopentyloxybiphenyl (derived from I and
AF4): 16.3 mg (85%); 1
H NMR (500 MHz, CDCl3) δ ppm
7.59 (d, J ) 2.2 Hz, 1H), 7.52 (m, 2H), 7.42 (m, 3H), 7.32
(m, 1H), 6.99 (d, J ) 8.4 Hz, 1H), 4.85 (m, 1H), 1.80-2.02
(m, 6H), 1.65 (m, 2H); MS (DCI/NH3) m/z 290 [M + NH4]+
;
RT ) 2.60.
3-Chloro-4-(1-methylbutoxy)biphenyl (derived from I
and AF5): 15.8 mg (82%); 1
H NMR (500 MHz, CDCl3) δ
ppm 7.60 (d, J ) 2.2 Hz, 1H), 7.53 (m, 2H), 7.42 (m, 3H),
7.32 (m, 1H), 6.99 (d, J ) 8.4 Hz, 1H), 4.41 (m, 1H), 1.83
(m, 1H), 1.40-1.70 (m, 3H), 1.36 (d, J ) 6.2 Hz, 3H), 0.96
(t, J ) 7.3 Hz, 3H); MS (DCI/NH3) m/z 292 [M + NH4]+
;
RT ) 2.65.
3-Chloro-4-(1,2-dimethylpropoxy)biphenyl (derived from
I and AF6): 13.1 mg (68%); 1
H NMR (500 MHz, CDCl3)
δ ppm 7.60 (d, J ) 2.5 Hz, 1H), 7.52 (m, 2H), 7.41 (m,
3H), 7.32 (m, 1H), 6.98 (d, J ) 8.4 Hz, 1H), 4.22 (m, 1H),
2.01 (m, 1H), 1.30 (d, J ) 6.2 Hz, 3H), 1.05 (d, J ) 6.6 Hz,
3H), 1.03 (d, J ) 6.9 Hz, 3H); MS (DCI/NH3) m/z 292 [M
+ NH4]+
; RT ) 2.66.
3-Chloro-4-(1-ethylpropoxy)biphenyl (derived from I
and AF7): 14.8 mg (77%); 1
H NMR (500 MHz, CDCl3) δ
ppm 7.60 (d, J ) 2.2 Hz, 1H), 7.52 (m, 2H), 7.42 (m, 3H),
7.32 (m, 1H), 6.98 (d, J ) 8.7 Hz, 1H), (4.21 (m, 1H), 1.76
(m, 4H), 1.01 (t, J ) 7.5 Hz, 6H); MS (DCI/NH3) m/z 292
[M + NH4]+
; RT ) 2.64.
3-Chloro-4-(2-methoxy-1-methylethoxy)biphenyl (de-
rived from I and AF8): 16.1 mg (83%); 1
H NMR (500
MHz, CDCl3) δ ppm 7.60 (d, J ) 2.5 Hz, 1H), 7.53 (m,
2H), 7.42 (m, 3H), 7.33 (m, 1H), 7.08 (d, J ) 8.7 Hz, 1H),
4.56 (m, 1H), 3.67 (dd, J ) 10.3, 5.9 Hz, 1H), 3.55 (dd, J
) 10.3, 4.7 Hz, 1H), 3.44 (s, 3H), 1.38 (d, J ) 6.2 Hz, 3H);
MS (DCI/NH3) m/z 294 [M + NH4]+
; RT ) 2.25.
3-Chloro-4-cyclohexyloxybiphenyl (derived from I and
AF9): 17.1 mg (85%); 1
H NMR (500 MHz, CDCl3) δ ppm
7.60 (d, J ) 2.2 Hz, 1H), 7.53 (m, 2H), 7.41 (m, 3H), 7.32
(m, 1H), 7.01 (d, J ) 8.4 Hz, 1H), 4.33 (m, 1H), 1.98 (m,
2H), 1.84 (m, 2H), 1.68 (m, 2H), 1.56 (m, 1H), 1.38 (m,
3H); MS (DCI/NH3) m/z 304 [M + NH4]+
; RT ) 2.70.
3-Chloro-4-(3-methylcyclopentyloxy)biphenyl [mixture
of cis/trans ∼1:2; not assigned] (derived from I and
AF10): 16.8 mg (84%); 1
H NMR (500 MHz, CDCl3) δ ppm
450 Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 Gentles et al.
14. (d, J ) 8.7 Hz, 1H), 7.41 (m, 9H), 7.35 (m, 2H), 6.93 (d, J
) 8.7 Hz, 1H), 4.98 (s, 2H); MS (DCI/NH3) m/z 337 [M +
H]+
, 354 [M + NH4]+
; RT ) 3.36.
2-(2-Fluoro-5-methylphenoxymethyl)biphenyl (derived
from II and P35-C42): 18.2 mg (77%); 1
H NMR (500 MHz,
CDCl3) δ ppm 7.65 (m, 1H), 7.39 (m, 7H), 7.33 (m, 1H),
6.92 (dd, J ) 11.2, 8.1 Hz, 1H), 6.65 (m, 1H), 6.59 (dd, J
) 8.1, 1.9 Hz, 1H), 4.98 (s, 2H), 2.21 (s, 3H); MS (DCI/
NH3) m/z 310 [M + NH4]+
; RT ) 3.11.
2-(Biphenyl-2-ylmethoxy)-4-methoxybenzoic acid meth-
yl ester (derived from II and P36-C46): 25.9 mg (92%);
1
H NMR (500 MHz, CDCl3) δ ppm 7.84 (m, 2H), 7.40 (m,
7H), 7.31 (m, 1H), 6.47 (dd, J ) 8.7, 2.5 Hz, 1H), 6.27 (d,
J ) 2.5 Hz, 1H), 5.03 (s, 2H), 3.86 (s, 3H), 3.74 (s, 3H);
MS (DCI/NH3) m/z 349 [M + H]+
, 366 [M + NH4]+
; RT )
2.88.
2-(2-Benzylphenoxymethyl)biphenyl (derived from II
and P37-C47): 17.1 mg (60%); 1
H NMR (500 MHz, CDCl3)
δ ppm 7.36 (m, 1H), 7.29 (m, 5H), 7.23 (m, 3H), 7.16 (m,
2H), 7.08 (m, 3H), 7.02 (m, 2H), 6.78 (t, J ) 7.3 Hz, 1H),
6.62 (d, J ) 8.4 Hz, 1H), 4.84 (s, 2H), 3.91 (s, 2H); MS
(DCI/NH3) m/z 368 [M + H]+
; RT ) 3.42.
6-(Biphenyl-2-ylmethoxy)-3,4-dihydro-2H-naphthalen-
1-one (derived from II and P38-C50): 23.3 mg (88%); 1
H
NMR (500 MHz, CDCl3) δ ppm 7.85 (d, J ) 8.7 Hz, 1H),
7.49 (m, 1H), 7.28 (m, 8H), 6.66 (dd, J ) 8.7, 2.2 Hz, 1H),
6.52 (d, J ) 2.5 Hz, 1H), 4.89 (s, 2H), 2.76 (t, J ) 6.1 Hz,
2H), 2.49 (t, J ) 6.6 Hz, 2H), 1.98 (m, 2H); MS (DCI/NH3)
m/z 329 [M + H]+
, 346 [M + NH4]+
; RT ) 2.92.
8-(Biphenyl-2-ylmethoxy)-2-methylquinoline, TFA salt
(derived from II and P39-C55): 2.2 mg (6%); 1
H NMR
(500 MHz, CDCl3) δ ppm 8.34 (d, J ) 8.4 Hz, 1H), 7.76
(m, 1H), 7.49 (d, J ) 8.7 Hz, 1H), 7.40 (m, 9H), 7.31 (m,
1H), 6.78 (dd, J ) 7.3, 1.4 Hz, 1H), 5.37 (s, 2H), 3.01 (s,
3H); MS (DCI/NH3) m/z 326 [M + H]+
; RT ) 1.99.
2-(2-Fluoro-4-nitrophenoxymethyl)biphenyl (derived
from II and P40-C60): 20.8 mg (79%); 1
H NMR (500 MHz,
CDCl3) δ ppm 7.96 (dd, J ) 10.5, 2.7 Hz, 1H), 7.93 (m,
1H), 7.60 (m, 1H), 7.40 (m, 8H), 6.80 (t, J ) 8.4 Hz, 1H),
5.11 (s, 2H); MS (DCI/NH3) m/z 341 [M + NH4]+
; RT )
2.99.
5-Acetyl-2-(biphenyl-2-ylmethoxy)benzamide (derived
from II and P41-C61): 20.0 mg (72%); 1
H NMR (500
MHz, CDCl3) δ ppm 8.78 (d, J ) 2.5 Hz, 1H), 8.04 (dd, J
) 8.7, 2.5 Hz, 1H), 7.57 (dd, J ) 7.5, 1.2 Hz, 1H), 7.30-
7.55 (m, 8H), 6.91 (d, J ) 8.7 Hz, 1H), 5.20 (s, 2H), 2.60
(s, 3H); MS (DCI/NH3) m/z 345 [M + H]+
, 363 [M +
NH4]+
; RT ) 2.31.
2-(Indan-5-ylmethoxyl)biphenyl (derived from II and
P42-C67): 16.0 mg (66%); 1
H NMR (500 MHz, CDCl3) δ
ppm 7.51 (m, 1H), 7.25 (m, 8H), 6.94 (d, J ) 8.1 Hz, 1H),
6.63 (d, J ) 1.2 Hz, 1H), 6.54 (dd, J ) 8.1, 2.2 Hz, 1H),
4.78 (s, 2H), 2.71 (m, 4H), 1.93 (m, 2H); MS (DCI/NH3)
m/z 301 [M + H]+
, 318 [M + NH4]+
; RT ) 3.34.
1-[4-Biphenyl-2-ylmethoxy)phenyl]-1H-imidazole (de-
rived from II and P43-C72): 13.3 mg (50%); 1
H NMR
(500 MHz, CDCL3) δ ppm 7.82 (br s, 1H), 7.62 (m, 1H),
7.39 (m, 8H), 7.25 (m, 2H), 7.20 (m, 2H), 6.93 (m, 2H),
4.98 (s, 2H); MS (DCI/NH3) m/z 327 [M + H]+
; RT ) 2.09.
2-(Biphenyl-2-ylmethoxy)dibenzofuran (derived from
II and P44-C73): 20.5 mg (72%); 1
H NMR (500 MHz,
CDCl3) δ ppm 7.84 (d, J ) 7.5 Hz, 1H), 7.68 (m, 1H), 7.52
(d, J ) 8.1 Hz, 1H), 7.43 (m, 8H), 7.36 (m, 2H), 7.30 (m,
2H), 7.02 (dd, J ) 9.0, 2.5 Hz, 1H), 5.04 (s, 2H); MS (DCI/
NH3) m/z 351 [M + H]+
, 368 [M + NH4]+
; RT ) 3.40.
7-(Biphenyl-2-ylmethoxy)-2,2-dimethyl-2,3-dihydroben-
zofuran (derived from II and P45-C83): 17.8 mg (67%);
1
H NMR (500 MHz, CDCl3) δ ppm 7.53 (m, 1H), 7.24 (m,
7H), 7.16 (m, 1H), 6.60 (dd, J ) 7.2, 0.6 Hz, 1H), 6.51 (t,
J ) 7.6 Hz, 1H), 6.41 (d, J ) 8.1 Hz, 1H), 4.92 (s, 2H),
2.87 (s, 2H), 1.36 (s, 6H); MS (DCI/NH3) m/z 330 [M]+
,
348 [M + NH4]+
; RT ) 3.16.
5-(Biphenyl-2-ylmethoxy)-2-methylbenzothiazole, TFA
salt (derived from II and P46-C88): 14.9 mg (41%); 1
H
NMR (500 MHz, CDCl3) δ ppm 7.64 (m, 2H), 7.41 (m, 7H),
7.34 (m, 2H), 7.02 (dd, J ) 8.7, 2.5 Hz, 1H), 5.01 (s, 2H),
2.84 (s, 3H); MS (DCI/NH3) m/z 332 [M + H]+
; RT ) 2.94.
5-[2-(Biphenyl-2-ylmethoxy)phenyl]isoxazole (derived
from II and P47-C90): 23.2 mg (88%); 1
H NMR (500 MHz,
CDCl3) δ ppm 8.22 (s, 1H), 8.00 (d, J ) 7.8 Hz, 1H), 7.61
(d, J ) 7.2 Hz, 1H), 7.44 (m, 2H), 7.34 (m, 7H), 7.06 (t, J
) 7.6 Hz, 1H), 6.86 (d, J ) 8.4 Hz, 1H), 6.66 (s, 1H), 5.09
(s, 2H); MS (DCI/NH3) m/z 328 [M + H]+
, 345 [M +
NH4]+
; RT ) 3.00.
6-(Biphenyl-2-ylmethoxy)benzo[1,3]oxathiol-2-one (de-
rived from II and P48-C99): 15.9 mg (59%); 1
H NMR (500
MHz, CDCl3) δ ppm 7.49 (m, 1H), 7.32 (m, 4H), 7.26 (m,
4H), 7.10 (d, J ) 9.4 Hz, 1H), 6.68 (m, 2H), 4.85 (s, 2H);
MS (DCI/NH3) m/z 334 [M]+
, 352 [M + NH4]+
; RT ) 3.04.
Acknowledgment. We thank Dr. Yvonne Martin for
many helpful discussions on the design of optimized diversity
sets and for her work in performing all of the cluster analyses
described in the text above. We also offer our sincere
gratitude to Patrick Wesdock of Applied Biosystems for his
considerable efforts in helping us enable our β-test version
of the Solaris 530 synthesizer and to Dr. Andrew Souers
and Dr. Douglas Kalvin for their help and advice in
reviewing the manuscript.
Supporting Information Available. Automated protocol
for syntheses and NMR spectra of various compounds. This
material is available free of charge via the Internet at http://
pubs.acs.org.
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456 Journal of Combinatorial Chemistry, 2002, Vol. 4, No. 5 Gentles et al.
